[2023-06-30 06:10:23,294] [INFO] DFAST_QC pipeline started.
[2023-06-30 06:10:23,298] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 06:10:23,298] [INFO] DQC Reference Directory: /var/lib/cwl/stgee5d1c2e-60d0-4ce6-bdb4-0168b10c92e9/dqc_reference
[2023-06-30 06:10:25,687] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 06:10:25,688] [INFO] Task started: Prodigal
[2023-06-30 06:10:25,688] [INFO] Running command: gunzip -c /var/lib/cwl/stg16d0fc55-1537-4b8f-ae1d-5510ea9a7f20/GCA_024276175.1_ASM2427617v1_genomic.fna.gz | prodigal -d GCA_024276175.1_ASM2427617v1_genomic.fna/cds.fna -a GCA_024276175.1_ASM2427617v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 06:10:32,861] [INFO] Task succeeded: Prodigal
[2023-06-30 06:10:32,862] [INFO] Task started: HMMsearch
[2023-06-30 06:10:32,862] [INFO] Running command: hmmsearch --tblout GCA_024276175.1_ASM2427617v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee5d1c2e-60d0-4ce6-bdb4-0168b10c92e9/dqc_reference/reference_markers.hmm GCA_024276175.1_ASM2427617v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 06:10:33,077] [INFO] Task succeeded: HMMsearch
[2023-06-30 06:10:33,079] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg16d0fc55-1537-4b8f-ae1d-5510ea9a7f20/GCA_024276175.1_ASM2427617v1_genomic.fna.gz]
[2023-06-30 06:10:33,112] [INFO] Query marker FASTA was written to GCA_024276175.1_ASM2427617v1_genomic.fna/markers.fasta
[2023-06-30 06:10:33,113] [INFO] Task started: Blastn
[2023-06-30 06:10:33,113] [INFO] Running command: blastn -query GCA_024276175.1_ASM2427617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee5d1c2e-60d0-4ce6-bdb4-0168b10c92e9/dqc_reference/reference_markers.fasta -out GCA_024276175.1_ASM2427617v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:10:33,800] [INFO] Task succeeded: Blastn
[2023-06-30 06:10:33,805] [INFO] Selected 22 target genomes.
[2023-06-30 06:10:33,805] [INFO] Target genome list was writen to GCA_024276175.1_ASM2427617v1_genomic.fna/target_genomes.txt
[2023-06-30 06:10:33,807] [INFO] Task started: fastANI
[2023-06-30 06:10:33,807] [INFO] Running command: fastANI --query /var/lib/cwl/stg16d0fc55-1537-4b8f-ae1d-5510ea9a7f20/GCA_024276175.1_ASM2427617v1_genomic.fna.gz --refList GCA_024276175.1_ASM2427617v1_genomic.fna/target_genomes.txt --output GCA_024276175.1_ASM2427617v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 06:10:47,697] [INFO] Task succeeded: fastANI
[2023-06-30 06:10:47,698] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee5d1c2e-60d0-4ce6-bdb4-0168b10c92e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 06:10:47,698] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee5d1c2e-60d0-4ce6-bdb4-0168b10c92e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 06:10:47,710] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 06:10:47,710] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 06:10:47,710] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Desulfarculus baarsii	strain=DSM 2075	GCA_000143965.1	453230	453230	type	True	78.7872	173	427	95	below_threshold
Dethiosulfatarculus sandiegensis	strain=SPR	GCA_000931935.2	1429043	1429043	type	True	76.8753	75	427	95	below_threshold
Deferrisoma camini	strain=S3R1	GCA_000526155.1	1035120	1035120	type	True	76.3042	77	427	95	below_threshold
Pseudodesulfovibrio indicus	strain=J2	GCA_001563225.1	1716143	1716143	type	True	76.2901	50	427	95	below_threshold
Desulfuromonas versatilis	strain=NIT-T3	GCA_019704135.1	2802975	2802975	type	True	75.3964	52	427	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 06:10:47,713] [INFO] DFAST Taxonomy check result was written to GCA_024276175.1_ASM2427617v1_genomic.fna/tc_result.tsv
[2023-06-30 06:10:47,713] [INFO] ===== Taxonomy check completed =====
[2023-06-30 06:10:47,713] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 06:10:47,714] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee5d1c2e-60d0-4ce6-bdb4-0168b10c92e9/dqc_reference/checkm_data
[2023-06-30 06:10:47,715] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 06:10:47,750] [INFO] Task started: CheckM
[2023-06-30 06:10:47,750] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024276175.1_ASM2427617v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024276175.1_ASM2427617v1_genomic.fna/checkm_input GCA_024276175.1_ASM2427617v1_genomic.fna/checkm_result
[2023-06-30 06:11:13,822] [INFO] Task succeeded: CheckM
[2023-06-30 06:11:13,824] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 5.56%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 06:11:13,848] [INFO] ===== Completeness check finished =====
[2023-06-30 06:11:13,849] [INFO] ===== Start GTDB Search =====
[2023-06-30 06:11:13,849] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024276175.1_ASM2427617v1_genomic.fna/markers.fasta)
[2023-06-30 06:11:13,849] [INFO] Task started: Blastn
[2023-06-30 06:11:13,849] [INFO] Running command: blastn -query GCA_024276175.1_ASM2427617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee5d1c2e-60d0-4ce6-bdb4-0168b10c92e9/dqc_reference/reference_markers_gtdb.fasta -out GCA_024276175.1_ASM2427617v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:11:14,898] [INFO] Task succeeded: Blastn
[2023-06-30 06:11:14,902] [INFO] Selected 7 target genomes.
[2023-06-30 06:11:14,902] [INFO] Target genome list was writen to GCA_024276175.1_ASM2427617v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 06:11:14,903] [INFO] Task started: fastANI
[2023-06-30 06:11:14,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg16d0fc55-1537-4b8f-ae1d-5510ea9a7f20/GCA_024276175.1_ASM2427617v1_genomic.fna.gz --refList GCA_024276175.1_ASM2427617v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024276175.1_ASM2427617v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 06:11:19,556] [INFO] Task succeeded: fastANI
[2023-06-30 06:11:19,568] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 06:11:19,568] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_018902755.1	s__SURF-10 sp018902755	84.32	337	427	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__SURF-10	95.0	99.98	99.96	0.97	0.96	6	-
GCA_018896025.1	s__SURF-10 sp018896025	84.2293	333	427	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__SURF-10	95.0	99.58	98.82	0.97	0.95	4	-
GCA_018819925.1	s__SURF-10 sp018819925	84.0304	321	427	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__SURF-10	95.0	99.87	99.83	0.95	0.93	4	-
GCA_003605055.1	s__SURF-10 sp003605055	82.6617	313	427	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__SURF-10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218705.1	s__JACRDC01 sp016218705	79.9214	251	427	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__JACRDC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016208115.1	s__JACRDC01 sp016208115	79.8982	243	427	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__JACRDC01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000143965.1	s__Desulfarculus baarsii	78.7872	173	427	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__Desulfarculus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 06:11:19,570] [INFO] GTDB search result was written to GCA_024276175.1_ASM2427617v1_genomic.fna/result_gtdb.tsv
[2023-06-30 06:11:19,571] [INFO] ===== GTDB Search completed =====
[2023-06-30 06:11:19,573] [INFO] DFAST_QC result json was written to GCA_024276175.1_ASM2427617v1_genomic.fna/dqc_result.json
[2023-06-30 06:11:19,574] [INFO] DFAST_QC completed!
[2023-06-30 06:11:19,574] [INFO] Total running time: 0h0m56s